The growth and structure of self-assembled adlayers of hexakis(n-dodecyl)-peri-hexabenzocoronene (HBC-C-12) adsorbed on highly ordered pyrolitic graphite (HOPG) decorated by an n-pentacontane (n-C50H102) monolayer have been investigated by scanning tunneling microscopy (STM). Whereas on HOPG the HBC-C-12 molecules readily self-assemble into a unique stable 2D structure, on the {n-C50H102 monolayer/graphite} system we observe morphological phase transitions with formation of time dependent a, 0, and gamma phases The initial a-phase is similar to that obtained on bare graphite, while intermediate and final gamma-structures present molecular dinners and rows, respectively. The observed two-dimensional polymorphism is due to weak interaction between HBC-C-12 molecules and n-C50H102-modified graphite substrate. Our results constitute an important step toward the control of the growth and structure of highly ordered monolayers of functional conjugated molecules by modifying the graphite surface with an n-alkane monolayer of appropriate chain length.